In reality it rarely works this way - there's plenty of systems which are falling apart due to "death of thousand cuts" type issues. You run a profiler and most of the queries are slow and there's no one obvious part to optimize - because developers over the years ignored basic optimizations and there are inefficiencies everywhere.

E.g., for a quick practice run, try optimizing Wordpress without making it a static page via caching - how many queries will you have to optimize and how much of a codebase rewrite will it be to make it significantly more performant?

in reality it does work that way.

the problem you describe is completely different and its more a measure of system health in its entirety of the DB. it can be easier to fix or harder depending on the precise cause. but that's a standard debugging skill which isn't strictly in the DBA skillset.

This is my experience especially with ORMs. It's really hard to optimize when your "top query time" list is just a list of your most frequently called methods, where there's no single obvious pathological case, but lots of little inefficiencies.